“Me standing there in handcuffs is the end result of something being shoved into a template when it never should have been,” Flanagan said.

Flanagan claims prosecutors stuffed a square peg into a round hole due to a weak case.

“Frankly, I do get emotional about it,” Flanagan said.

Emotions were raw as Flanagan sat down with McLogan, his first interview since he and two other high-ranking commanders resigned from the force in April. They are accused in a conspiracy to scuttle a burglary probe of the son of financial benefactor of police. Prosecutors said the teen was to be arrested for stealing audiovisual equipment from his high school, but the commanders thwarted Zachary Parker’s arrest to curry favor with his dad, Gary.

“I did nothing wrong. I did not violate my oath of office. There is nothing here, nothing,” Flanagan said.

The former commander said he wants his case thrown out. New e-mails have recently surfaced that indicate the school may have wanted to handle the matter internally: “Put everything on hold” until further notice the principal wrote.

“Failure to disclose these e-mails, if they knew about it, raises very serious questions about the ethical nature of the indictment and the prosecution of this case,” defense attorney Bruce Barket said.

However, prosecutors are confident in their case, pointing out the school has said publicly it wanted Zachary Parker arrested.

Flanagan, they said, had e-mail problems of his own.

When asked if Gary Parker dropped off gift cards to Morton’s steakhouse specifically for Flanagan and his wife, the former commander said “I never used those gift cards.”

“It was a huge number thrown out there. Exactly, it looks like Gary Parker spent $17,000 on Bill Flanagan. That didn’t happen. There were 20 or 30 people at those lunches or dinners,” Flanagan said in response.

Flanagan said he wants to reclaim and restore his once-stellar reputation and is now asking a judge to investigate.

District Attorney Rice’s office responded, saying: “These officers illegally conspired to prevent the arrest of a police benefactor’s son who stole more than $11,000 worth of electronics. We remain confident in the case against them.”